Support for multiscale simulations with molecular dynamics

We present a reusable solution that supports users in combining single-scale models to create a multiscale application. Our approach applies several multiscale programming tools to allow users to compose multiscale applications using a graphical interface, and provides an easy way to execute these multiscale applications on international production infrastructures. Our solution extends the general purpose scripting approach of the GridSpace platform with simple mechanisms for accessing production resources, provided by the Application Hosting Environment (AHE). We apply our support solution to construct and execute a multiscale simulation of clay-polymer nanocomposite materials, and showcase its benefit in reducing the effort required to do a number of time-intensive user tasks. © 2013 The Authors. Published by Elsevier B.V

Multiscale modeling of heat conduction in graphene laminates

We developed a combined atomistic-continuum hierarchical multiscale approach to explore the effective thermal conductivity of graphene laminates. To this aim, we first performed molecular dynamics simulations in order to study the heat conduction at atomistic level. Using the non-equilibrium molecular dynamics method, we evaluated the length dependent thermal conductivity of graphene as well as the thermal contact conductance between two individual graphene sheets. In the next step, based on the results provided by the molecular dynamics simulations, we constructed finite element models of graphene laminates to probe the effective thermal conductivity at macroscopic level. A similar methodology was also developed to study the thermal conductivity of laminates made from hexagonal boron-nitride (h-BN) films. In agreement with recent experimental observations, our multiscale modeling confirms that the flake size is the main factor that affects the thermal conductivity of graphene and h-BN laminates. Provided information by the proposed multiscale approach could be used to guide experimental studies to fabricate laminates with tunable thermal conduction properties

Concurrent coupling of atomistic simulation and mesoscopic hydrodynamics for flows over soft multi-functional surfaces

We develop an efficient parallel multiscale method that bridges the atomistic and mesoscale regimes, from nanometer to micron and beyond, via concurrent coupling of atomistic simulation and mesoscopic dynamics. In particular, we combine an all-atom molecular dynamics (MD) description for specific atomistic details in the vicinity of the functional surface, with a dissipative particle dynamics (DPD) approach that captures mesoscopic hydrodynamics in the domain away from the functional surface. In order to achieve a seamless transition in dynamic properties we endow the MD simulation with a DPD thermostat, which is validated against experimental results by modeling water at different temperatures. We then validate the MD-DPD coupling method for transient Couette and Poiseuille flows, demonstrating that the concurrent MD-DPD coupling can resolve accurately the continuum-based analytical solutions. Subsequently, we simulate shear flows over polydimethylsiloxane (PDMS)-grafted surfaces (polymer brushes) for various grafting densities, and investigate the slip flow as a function of the shear stress. We verify that a "universal" power law exists for the sliplength, in agreement with published results. Having validated the MD-DPD coupling method, we simulate time-dependent flows past an endothelial glycocalyx layer (EGL) in a microchannel. Coupled simulation results elucidate the dynamics of EGL changing from an equilibrium state to a compressed state under shear by aligning the molecular structures along the shear direction. MD-DPD simulation results agree well with results of a single MD simulation, but with the former more than two orders of magnitude faster than the latter for system sizes above one micron.Comment: 11 pages, 12 figure